Image inspection¶

In [1]:
%load_ext autoreload
%autoreload 2
In [2]:
from scip_workflows.common import *
from aicsimageio import AICSImage
In [3]:
import re
In [4]:
try:
    input_file = snakemake.input[0]
    output = snakemake.output[0]
except NameError:
    input_file = Path("/home/maximl/scratch/data/vsc/datasets/cd7/800/Experiment-800.czi")
    output = Path("/home/maximl/scratch/data/vsc/datasets/cd7/800/scenes.txt")
In [5]:
im = AICSImage(input_file, reconstruct_mosaic=False)
In [6]:
pattern = r"P(?P<position>[0-9]+)-(?P<exp>[A-Z])(?P<replicate>[0-9])"
df = pandas.DataFrame(map(lambda a: re.match(pattern, a).groupdict(), im.scenes))
df = df[df["exp"] == "D"]
df["position"] = df["position"].astype(int)
df["replicate"] = df["replicate"].astype(int)
df = df.set_index(["replicate", "position"])
In [7]:
im.set_scene("P1-D1")
In [18]:
fig, ax = plt.subplots(dpi=150)
ax.imshow(numpy.max(im.get_image_data("ZXY", C=5), axis=0), origin="lower", cmap="Greys")
ax.set_axis_off()
In [28]:
def draw_tile(data, channel, color=None, hue=None):
    p, rep = data.position.iloc[0], data.replicate.iloc[0]
    im.set_scene(f"P{p}-D{rep}")
    
    ax = plt.gca()
    
    ax.imshow(numpy.max(im.get_image_data("ZXY", C=channel), axis=0), origin="lower", cmap="viridis")
    ax.set_axis_off()
    print(f"{p}-{rep}", end=" ")
In [29]:
# DAPI

grid = seaborn.FacetGrid(data=df.reset_index(), col="position", row="replicate", margin_titles=True)
grid.map_dataframe(draw_tile, channel=0)
for ax in grid.axes.ravel():
    ax.set_axis_off()

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In [35]:
bad_indices = [
    (2, 1), (2,15), (2,21),
    (3, 25),
    (4, 21), (4, 25),
    (5, 25), (5, 21)
]

df = df.drop(index=bad_indices)
In [18]:
# CD45 - EGFP

grid = seaborn.FacetGrid(data=df.reset_index(), col="position", row="replicate", margin_titles=True)
grid.map_dataframe(draw_tile, channel=1)
for ax in grid.axes.ravel():
    ax.set_axis_off()

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In [37]:
bad_indices = [
    (2, 8)
]

df = df.drop(index=bad_indices)
In [20]:
# siglec8 - RPe

grid = seaborn.FacetGrid(data=df.reset_index(), col="position", row="replicate", margin_titles=True)
grid.map_dataframe(draw_tile, channel=2)
for ax in grid.axes.ravel():
    ax.set_axis_off()

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In [38]:
bad_indices = [
    (2, 3), (2,23),
    (5, 5)
]

df = df.drop(index=bad_indices)
In [36]:
# CD15 - APC

grid = seaborn.FacetGrid(data=df.reset_index(), col="position", row="replicate", margin_titles=True)
grid.map_dataframe(draw_tile, channel=3)
for ax in grid.axes.ravel():
    ax.set_axis_off()

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In [52]:
with open(output, "w") as fh:
    fh.write("    scenes:\n")
    for s in df.reset_index().apply(lambda r: f"P{r.position}-{r.exp}{r.replicate}", axis=1).values.tolist():
        fh.write(f"      - {s}\n")
In [ ]: